Matrix Of Pairwise Genetic Distances Research Articles

Does Triatoma brasiliensis occupy the same environmental niche space as Triatoma melanica?

BackgroundTriatomines (Hemiptera, Reduviidae) are vectors of Trypanosoma cruzi, the causative agent of Chagas disease, one of the most important vector-borne diseases in Latin America. This study compares the environmental niche spaces of Triatoma brasiliensis and Triatoma melanica using ecological niche modelling and reports findings on DNA barcoding and wing geometric morphometrics as tools for the identification of these species.MethodsWe compared the geographic distribution of the species using generalized linear models fitted to elevation and current data on land surface temperature, vegetation cover and rainfall recorded by earth observation satellites for northeastern Brazil. Additionally, we evaluated nucleotide sequence data from the barcode region of the mitochondrial cytochrome c oxidase subunit I (CO1) and wing geometric morphometrics as taxonomic identification tools for T. brasiliensis and T. melanica.ResultsThe ecological niche models show that the environmental spaces currently occupied by T. brasiliensis and T. melanica are similar although not equivalent, and associated with the caatinga ecosystem. The CO1 sequence analyses based on pair wise genetic distance matrix calculated using Kimura 2-Parameter (K2P) evolutionary model, clearly separate the two species, supporting the barcoding gap. Wing size and shape analyses based on seven landmarks of 72 field specimens confirmed consistent differences between T. brasiliensis and T. melanica.ConclusionOur results suggest that the separation of the two species should be attributed to a factor that does not include the current environmental conditions. However, as the caatinga is a biome that has existed in the area for at least the last 18,000 years, past conditions might have had an influence in the speciation process. The DNA Barcoding approach may be extended to these members of the subfamily Triatominae.

Macrogeographic genetic variability in the Gastropod Mollusk Littorina sitkana from the Northwest Pacific

Variation at four highly polymorphic allozyme loci (inorganic pyrophosphatase, peptidase, and two esterase loci) was examined in 25 settlements of the marine snail Littorina sitkana (Mollusca, Gastropoda). The sampling localities covered a wide part of the species range: from the Peter the Great Bay (the Sea of Japan) at the southwest to the Mednyi Island (Commander Islands) at the northeast. Like other littorines lacking the pelagic stage, L. sitkana was characterized by significant genetic differentiation (G(ST) for the pooled sample was 0.310). Cluster analysis and nonmetric multidimensional scaling conducted on a matrix of pairwise genetic distances between all of the settlements studied revealed four genetically different groups: southern Primorye, northern Prymorye, Sakhalin, and Kuril-Commanders. The population-genetic structure of the L. sitkana settlements is close to that described by the isolation-by-distance and stepping-stone models: the geographic and the genetic distances between the most settlements examined are distinctly correlated.

Multilocus sequence typing analysis of human and animal Clostridium difficile isolates of various toxigenic types.

A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 72 Clostridium difficile isolates from various hosts, geographic sources, PCR ribotypes, and toxigenic types (determined by PCR targeting tcdA and tcdB genes). MLST was performed by DNA sequence analysis of seven housekeeping genes (aroE, ddl, dutA, tpi, recA, gmk, and sodA). The number of alleles ranged from five (dutA and ddl) to eleven (recA). Allelic profiles allowed the definition of 34 different sequence types (STs). These STs lacked correlation with geographic source but were well correlated to toxigenic type. The dendrogram generated from a matrix of pairwise genetic distances showed that animal isolates did not constitute a distinct lineage from human isolates and that there was no hypervirulent lineage within the population of toxigenic human isolates (isolates recovered from pseudomembranous colitis and antibiotic-associated diarrhea did not cluster in distinct lineages). However, A(-) B(+) variant isolates shared the same ST that appeared as a divergent lineage in the population studied, indicating a single evolutionary origin. The population structure was further examined by analysis of allelic polymorphism. The dendrogram generated from composite sequence-based analysis revealed a homogeneous population associated with three divergent lineages, one of which was restricted to A(-) B(+) variant isolates. C. difficile exhibited a clonal population structure, as revealed by the estimation of linkage disequilibrium (Ia) between loci. The analysis of alleles within clonal complexes estimated that point mutation generated new alleles at a frequency eightfold higher than recombinational exchange, and the congruence of the dendrograms generated from separate housekeeping loci confirmed the mutational evolution of this species.

Multilocus genetic relationships between clinical and environmental Aeromonas strains

Allelic variations in the chromosomal genome of 120 isolates of motile Aeromonas (A. hydrophila, A. sobria and A. caviae) and eight reference strains with one Plesiomonas shigelloides were assessed by analysis of electrophoretically demonstrable polymorphism in 16 genes encoding metabolic enzymes. The strains were collected from humans (n = 59) and from the aquatic environment (n = 61) in canton Tessin, Switzerland. Clustering of the electrophoretic types (ET) from a matrix of pairwise genetic distances, based on the 16 enzyme loci, confirmed the genetic distinctness of the three species. Furthermore, A. hydrophila and A. sobria were divided in three and two groups respectively. For each species clinical strains were well differentiated from those collected in the environment.

Multilocus genetic relationships between clinical and environmentalAeromonasstrains

Allelic variations in the chromosomal genome of 120 isolates of motile Aeromonas (A. hydrophila, A. sobria and A. caviae) and eight reference strains with one Plesiomonas shigelloides were assessed by analysis of electrophoretically demonstrable polymorphism in 16 genes encoding metabolic enzymes. The strains were collected from humans (n = 59) and from the aquatic environment (n = 61) in canton Tessin, Switzerland. Clustering of the electrophoretic types (ET) from a matrix of pairwise genetic distances, based on the 16 enzyme loci, confirmed the genetic distinctness of the three species. Furthermore, A. hydrophila and A. sobria were divided in three and two groups respectively. For each species clinical strains were well differentiated from those collected in the environment.

Clonal diversity and relationships among strains of Yersinia enterocolitica.

Allelic variation in the chromosomal genome of 81 isolates of Yersinia enterocolitica and single isolates of Yersinia intermedia, Yersinia frederiksenii, Yersinia mollaretii, and Yersinia kristensenii was assessed by analysis of electrophoretically demonstrable polymorphism in 21 genes encoding metabolic enzymes. Eighteen distinctive multilocus genotypes (electrophoretic types [ETs]) were identified. Clustering of the ETs from a matrix of pairwise genetic distances, based on the 21 enzyme loci, confirmed the genetic distinctness of serogroup 3 isolates of Y. intermedia, Y. frederiksenii, Y. mollaretii, and Y. kristensenii and identified another serogroup 3 isolate that was also not a member of Y. enterocolitica. The 13 ETs of Y. enterocolitica clustered into two groups: cluster A, which included eight ETs represented by isolates of serogroups 1; 2; 3; 5,27; and 9, and cluster B, which included four ETs represented by isolates of serogroups 8, 13, and 21. Clones of cluster A were found to be distributed worldwide, but those of cluster B were largely restricted to North America. Isolates of genotypes belonging to cluster B were lethal to mice, whereas those of cluster A were not, suggesting an influence of the chromosomal background on the virulence of Y. enterocolitica.